A known "feature" of the MySQL connection pool manager and the JDBC driver means that MySQL times out connections that have been idle for a long period of time but the JDBC driver cannot easily re-establish these.

If you are seeing exceptions such as the following in the Protege server logs (<Protege_Install>/logs):

com.mysql.jdbc.CommunicationsException: Communications link failure

It is likely that the Protege server has just tried to use a JDBC database connection that MySQL has culled. There is no complete solution to this at the present time, and the work around is to set the connection timeout on the MySQL database server very high, e.g. 5+ days and have the Protege server restarted weekly to ensure that the connections are regularly reset.